How to get Color and Z-Depth from Viewer Node?
I am trying to do something similar. I (think) I made it by connecting the Render Image to Viewer Image and by connecting Render Z to Viewer Alpha. I used your code as a starting point.

import bpy
import numpy as np

bpy.context.scene.render.use_compositing = True
bpy.context.scene.use_nodes = True
tree = bpy.context.scene.node_tree
links = tree.links

for n in tree.nodes:
    tree.nodes.remove(n)
rl = tree.nodes.new('CompositorNodeRLayers')      

vl = tree.nodes.new('CompositorNodeViewer')   
vl.use_alpha = True
links.new(rl.outputs[0], vl.inputs[0])  # link Renger Image to Viewer Image
links.new(rl.outputs[2], vl.inputs[1])  # link Render Z to Viewer Alpha

#render
bpy.context.scene.render.resolution_percentage = 100 #make sure scene height and width are ok (edit)
bpy.ops.render.render()

#get the pixels and put them into a numpy array
pixels = np.array(bpy.data.images['Viewer Node'].pixels)
print(len(pixels))

width = bpy.context.scene.render.resolution_x 
height = bpy.context.scene.render.resolution_y

#reshaping into image array 4 channel (rgbz)
image = pixels.reshape(height,width,4)

#depth analysis...
z = image[:,:,3]
zf = z[z&lt;1000] #
print(np.min(zf),np.max(zf))


I wouldn't use Viewer Depth channel since Image pixels (RGBA) are floats whereas depth are ints.